2CHN | pdb_00002chn

Bacteroides thetaiotaomicron hexosaminidase with O-GlcNAcase activity- NAG-thiazoline complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.226 (Depositor) 
  • R-Value Work: 
    0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structure and Mechanism of a Bacterial B-Glucosaminidase Having O-Glcnacase Activity

Dennis, R.J.Taylor, E.J.Macauley, M.S.Stubbs, K.A.Turkenburg, J.P.Hart, S.J.Black, G.N.Vocadlo, D.J.Davies, G.J.

(2006) Nat Struct Mol Biol 13: 365

  • DOI: https://doi.org/10.1038/nsmb1079
  • Primary Citation Related Structures: 
    2CHN, 2CHO

  • PubMed Abstract: 

    O-GlcNAc is an abundant post-translational modification of serine and threonine residues of nucleocytoplasmic proteins. This modification, found only within higher eukaryotes, is a dynamic modification that is often reciprocal to phosphorylation. In a manner analogous to phosphatases, a glycoside hydrolase termed O-GlcNAcase cleaves O-GlcNAc from modified proteins. Enzymes with high sequence similarity to human O-GlcNAcase are also found in human pathogens and symbionts. We report the three-dimensional structure of O-GlcNAcase from the human gut symbiont Bacteroides thetaiotaomicron both in its native form and in complex with a mimic of the reaction intermediate. Mutagenesis and kinetics studies show that the bacterial enzyme, very similarly to its human counterpart, operates via an unusual 'substrate-assisted' catalytic mechanism, which will inform the rational design of enzyme inhibitors.


  • Organizational Affiliation
    • York Structural Biology Laboratory, Department of Chemistry, University of York, York Y010 5YW, UK.

Macromolecule Content 

  • Total Structure Weight: 169.13 kDa 
  • Atom Count: 11,738 
  • Modeled Residue Count: 1,305 
  • Deposited Residue Count: 1,456 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLUCOSAMINIDASE
A, B
716Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
EC: 3.2.1.52 (PDB Primary Data), 3.2.1.169 (UniProt)
UniProt
Find proteins for Q89ZI2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q89ZI2 
Go to UniProtKB:  Q89ZI2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89ZI2
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GLUCOSAMINIDASE
C, D
12Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
EC: 3.2.1.52

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NGT

Query on NGT



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B]
3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
C8 H13 N O4 S
DRHXTSWSUAJOJZ-FMDGEEDCSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
J [auth B],
K [auth C],
L [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
UNK
Query on UNK
C, D
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.226 (Depositor) 
  • R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.714α = 75.34
b = 94.544β = 93.86
c = 99.479γ = 77.07
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-08
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary